From 7e3e714d3c4f7d7db0930b365c6cac4e9ea45bba Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 6 Jan 2010 19:34:10 +0000 Subject: [PATCH] Moving experimental annotations from core to oneoffs git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2528 348d0f76-0448-11de-a6fe-93d51630548a --- .../annotator/ProportionOfNonrefBasesSupportingSNP.java | 6 ++++-- .../annotator/ProportionOfRefSecondBasesSupportingSNP.java | 7 ++++--- .../annotator/ProportionOfSNPSecondBasesSupportingRef.java | 7 ++++--- 3 files changed, 12 insertions(+), 8 deletions(-) rename java/src/org/broadinstitute/sting/{gatk => oneoffprojects}/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java (92%) rename java/src/org/broadinstitute/sting/{gatk => oneoffprojects}/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java (93%) rename java/src/org/broadinstitute/sting/{gatk => oneoffprojects}/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java (93%) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java similarity index 92% rename from java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java index 2c0925923..6234e59f5 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java @@ -1,6 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.annotator; +package org.broadinstitute.sting.oneoffprojects.walkers.annotator; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.Pair; @@ -8,6 +9,7 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; +import org.broadinstitute.sting.gatk.walkers.annotator.*; import java.util.Map; @@ -18,7 +20,7 @@ import java.util.Map; * Time: 2:48:15 PM * To change this template use File | Settings | File Templates. */ -public class ProportionOfNonrefBasesSupportingSNP implements VariantAnnotation{ +public class ProportionOfNonrefBasesSupportingSNP implements VariantAnnotation { private String KEY_NAME = "prop_nonref_that_are_snp"; public String getKeyName() { return KEY_NAME; } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java similarity index 93% rename from java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java index 2da68d331..dd3219ba2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java @@ -1,6 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.annotator; +package org.broadinstitute.sting.oneoffprojects.walkers.annotator; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.Pair; @@ -18,7 +19,7 @@ import java.io.PrintWriter; import java.io.FileOutputStream; import java.util.List; import java.util.Map; - +import org.broadinstitute.sting.gatk.walkers.annotator.*; /** * Created by IntelliJ IDEA. * User: chartl @@ -26,7 +27,7 @@ import java.util.Map; * Time: 2:18:43 PM * To change this template use File | Settings | File Templates. */ -public class ProportionOfRefSecondBasesSupportingSNP implements VariantAnnotation{ +public class ProportionOfRefSecondBasesSupportingSNP implements VariantAnnotation { private String KEY_NAME = "ref_2bb_snp_prop"; private boolean USE_MAPQ0_READS = false; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java similarity index 93% rename from java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java index 5c7894949..33216fdf0 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java @@ -1,8 +1,9 @@ -package org.broadinstitute.sting.gatk.walkers.annotator; +package org.broadinstitute.sting.oneoffprojects.walkers.annotator; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation; import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.Pair; @@ -11,7 +12,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; import java.util.Map; - + import org.broadinstitute.sting.gatk.walkers.annotator.*; /** * Created by IntelliJ IDEA. * User: chartl @@ -19,7 +20,7 @@ import java.util.Map; * Time: 2:42:05 PM * To change this template use File | Settings | File Templates. */ -public class ProportionOfSNPSecondBasesSupportingRef implements VariantAnnotation{ +public class ProportionOfSNPSecondBasesSupportingRef implements VariantAnnotation { public String KEY_NAME = "SNP_2B_SUPPORT_REF"; public boolean USE_MAPQ0_READS = false; public String debug_file = "/humgen/gsa-scr1/chartl/temporary/ProportionOfRefSecondBasesSupportingSNP.debug.txt";